Guys, how can I use the tables, produced by the Galaxy-embedded RUVseq? Its output looks like this:
batch_effects_control_method_k1 identifier condition W_1 Counts_s1.tabular Cont -0.343905680583747 Counts_s2.tabular Cont 0.581535965604329 Counts_s3.tabular Cont -0.285812794268053 Counts_s4.tabular Treat -0.25027199487464 Counts_s5.tabular Treat -0.271891634519469 Counts_s6.tabular Treat 0.570346138641578
... and similar tables for the "batch_effects_replicate_method_k1" and "batch_effects_replicate_method_k1".
How can I use these tables for differential expression analysis, ideally, in the Galaxy itself?
(I tried to run RUVseq in the R-studio too, as it is written in the tutorial (http://bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf), but, for some reason, it didn't work).
Thanks in advance for any help.